Digital Collections

Thu Sep 11 16:18:48 2014

Logo for Swedish Museum of Natural History Swedish Museum of Natural History

BIO - Bioinformatics and Genetics

BIO is a unit within the Research Department at the Swedish Museum of Natural History, led by Professor Fredrik Ronquist and organized in three groups:

Swedish DINA Team (from NRM-BIO)

Karin Karlsson Markus Englund Kevin Holsten Stefan Daume
Karin Karlsson Markus Englund Kevin Holston Stefan Daume
Team Leader Domain Specialist Domain Specialist Systems Architect
Ida Li Ingimar Erlingsson Markus Skyttner
Ida Li Ingimar Erlingsson Markus Skyttner
Developer Developer Developer

The DINA project (started 2006)

The DINA project (DINA from DIgital NAtural history collections) is an international effort to develop a common collection management system to be used at a national scale, replacing independent databases and helping to make dataset broadly accessible for research and public use.

The DINA project applies an international perspective towards achieving this goal, which has been apparent since its initial efforts to improve the Specify 6 data model in the context of biodiversity informatics community standards and technological advances.

The DINA project strategy

We are using an open source oriented development methodology, cooperating internationally in a decentralized fashion, aiming to:

  • pool developer resources
  • improve software quality and transparency.
  • provide a full-featured relevant feature set

The DINA spirit

Through open discussions of DINA objectives and activities, the project has benefited from a broad diversity of perspectives and technical contributions beyond its resource limitations.

Technical development of DINA system components is the cohesive theme underlying open-source software development among members of the DINA consortium.

The DINA consortium

This network of developer groups, focused on data and workflows at natural history collections, recognizes the potential for presenting a de-facto standard for collection management systems beyond the needs of user groups within the respective partner organisations.

While each DINA partner will have to focus on the institutional users they are serving, the system design should reflect this ambition.

The DINA architecture

Specifically, the architectural approach should accommodate future user demands as best as possible.

It should aim at providing a common collaborative framework that invites contributions from new partners which may become full or associated members of the DINA consortium.

  • Web-oriented, public accessibility, using open source technology stacks
  • Service oriented architecture favoring RESTful web services (impl with Java, Python)
  • Using international standards, like Darwin Core and Audubon

Swedish DINA partners

DINA International Council

New partners are welcome to join the collaboration!

Data flows to GBIF

gbif.se

Data flows directly from the DINA system to GBIF via the Swedish GBIF node.

DINA Web UI components (operational)

Naturav.se

  • a taxonomic module for multiple taxonomies (UTARTU, EST, UI integrated in Pluto-F)
  • Naturfynd - the inventory client
  • Naturarv - the DINA web search portal
  • The Naturalist - the species information pages
  • Swedish DNA-key portal

DINA Web data APIs

Online currently:

Work in progress:

  • API for coll mgm?
  • API for BLAST?
  • API for literature?

OAuth v 2 support?

DINA Web UI components (WIP)

Naturav.se

  • a multimedia server module (NRM, SWE)
  • a distributed biomediabank repository (UCPH, DEN)
  • a DNA module (Agriculture Canada, Ottawa, CAN)
  • an RDF module (Museum für Naturkunde, Berlin, GE)

DETAILS ON SPECIFIC MODULES FOLLOW

The following slides provide more details on specific modules mentioned earlier

Collections management client - the Specify Web Client

  • aka Specify Web Client, alpha released, beta planned for Spring 2014
  • complete system for professional mgm of collections (objects, loans, images etc)
  • UI resembling Specify 6 Java thick client, esp in parts developed in Kansas
  • Components developed at the Swedish Museum of Natural History are designed for DINA Web

On hold! - waiting for stable release that can address user needs

Batch inventory client - Naturfynd

Batch processing

  • aka Naturfynd, released in Dec 2012
  • for researchers and collection staff dealing with large batch inventory projects
  • supports fast digitization of large amounts of objects
  • examples: Markfaunainventeringen, Swedish Malaise Trap Project

DINA web portal - Naturarv

Naturav.se

  • aka Naturarv.se, released in May 2013, a search portal for DINA Web system
  • for researchers and general public, but also useful for DINA staff for
    • getting an overview and do searches for objects
    • spotting of anomalies and reporting errors to staff
    • later versions have planned support for images and loans

The Naturalist

naturforskaren.se

  • aka naturforskaren.se, released in 2012 in November, updated in 2013 in November
  • EU-financed project, developed in cooperation with Finland and Estonia
  • Collects popular species information related to scandobaltic species, harvests from and links to various other systems
  • Now integrating Estonian developed taxonomy module

Swedish DNA-key

dna-key.se

  • Released 2014 in January
  • Financed by FORMAS and associated with CGI - Swedish Centre for Genetic Identification
  • Species determinations based on gene sequence matching against Swedish ref data and BOLD (GenBank)
  • Linked to voucher information in DINA (maps, images, collection data)
  • Linked to species information in The Naturalist (naturforskaren.se)

Curious for more about DINA?

Interested in participating in module development?

There is a great deal of flexibility in developing DINA modules and API:s of interest to EU-BON partners and other collaborators…

Possible activities may include development of a literature module (possibly based on Bibliography of Life, PenSoft?), functionality to support mass digitization, data mobilization, etc.

DINA Specify Technical Workshop

A DINA - Specify technical workshop under the auspices of EU BON be held in the autumn

  • Date: The date is set for 15-17 September 2014
  • Location: Stockholm, Sweden

Another workshop is planned for end users (Milestone 3), tentatively in January 2016.

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